Thanks for the question. If you're processing payments through Intuit, the default account payments will go to will always be Undeposited Funds. That's because, in your real world banking, those funds have not been deposited to your bank yet. Once those deposits are made, they should move from Undeposited Funds to your bank account in QuickBooks Online. Unfortunately, there is not a way to change that as long as you are processing with an Intuit merchant service account.
I have also been trying to figure out the same thing. The issue on our end is that even after the payments are deposited into our checking account, they remain under Undeposited Funds and there is no way to manually change them (ie when reviewing transactions in the Banking section, reconciling the bank statement etc.) It just seems not right to have these transactions showing up as Undeposited funds when we run that Chart of Accounts report or the monthly reconciling. Is there no way to change this setting?